Add CLI for coSMicQC

[d33bs]

Description

This PR adds a CLI for coSMicQC through the use of fire. This work depends on changes from #32 . Along the journey towards these changes I discovered there were challenges in displaying pd.DataFrame's (or related SCDataFrame's) through fire CLI's. As a result, I added a patch inspired from work in google/python-fire#446 by reassigning the _PrintResult function to match the contents of the fix. Once the fix is merged in fire we should remove the patch and rely on fire for these changes. When/if these changes are merged, I'll create an issue to track this so we don't forget to take action here.

Along with these changes some docs were fixed.

This should be reviewed and merged after #32

Closes #14
Closes #37

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• I have read and followed the CONTRIBUTING.md guidelines.
• I have searched for existing content to ensure this is not a duplicate.
• I have performed a self-review of these additions (including spelling, grammar, and related).
• These changes pass all pre-commit checks.
• I have added comments to my code to help provide understanding
• I have added a test which covers the code changes found within this PR
• I have deleted all non-relevant text in this pull request template.

[d33bs]

In chatting with @jenna-tomkinson, we discussed that getting a file-based output would potentially be more useful than text-based output. The filename could use the input filename as the basis for output filename, for example example.csv would become example.identify_outliers.parquet

[d33bs]

Thinking on file-based output a little more made me feel that that work might be best served after merging #32 and this PR. Generally, I'm worried that there may be complex scenarios where one would want a file vs not. It also might be possible to control the export of files through a similar mechanism to pd.DataFrame, i.e. pd.DataFrame.to_parquet(...), etc. which could avoid us having to maintain additional code. Created #37 as a result.

Decided to implement this within the same PR.

[jenna-tomkinson]

I am approving this PR since I do not see any issues in the code that looks to cause any bugs. I left a lot of comments with questions and suggestions for increasing clarity for a reader of the code. Nice job! 🎉

[d33bs]

Thanks @jenna-tomkinson for the review! I've addressed your comments and will now merge this in.